Model type
Metagenomic functional profiling pipeline
Pipeline
HUMAnN
HUMAnN profiles microbial gene functions and pathways from metagenomic or metatranscriptomic reads.
Sources
biobakery/humann: readme.md · readme.md: description, Main workflow, Download the databases and normalization documentationHow it worksHUMAnN workflow
Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.
Sources
biobakery/humann: readme.md · readme.md: description, Main workflow, Download the databases and normalization documentationAt a glance
Inputs
Short DNA/RNA reads or supported preprocessed alignment/profile inputs.
Sources
biobakery/humann: readme.md · readme.md: description, Main workflow, Download the databases and normalization documentationOutputs
Gene-family and pathway abundance/coverage tables, including organism-stratified outputs.
Sources
biobakery/humann: readme.md · readme.md: description, Main workflow, Download the databases and normalization documentationSource reviewed · Automated source review, 2026-09-16. All specifications and missing details
Evaluations and results
Release 2026-09-17-d277315f7d76 · 0 evaluations · 0 metric rows. Different protocols are not a single leaderboard.
No evaluations linked in this release.
How it works
How it works
HUMAnN profiles microbial gene functions and pathways from metagenomic or metatranscriptomic reads. Reference-based functional profiling pipeline with nucleotide and translated search against configured databases. The documented inputs are short DNA/RNA reads or supported preprocessed alignment/profile inputs. The output consists of gene-family and pathway abundance/coverage tables, including organism-stratified outputs.
Sources
biobakery/humann: readme.md · readme.md: description, Main workflow, Download the databases and normalization documentationVersions and reproducibility
HUMAnN 3.0 paper and implementation; nucleotide/protein database versions must be preserved separately. Read files and search-database size; no fixed model context.
Sources
biobakery/humann: readme.md · readme.md: description, Main workflow, Download the databases and normalization documentationStrengths and limitations
Strengths supported by sources
- Connects community sequencing data to interpretable functional and pathway profiles.
Sources
biobakery/humann: readme.md · readme.md: description, Main workflow, Download the databases and normalization documentation
Limitations and conditions
- Reference coverage and normalization affect interpretation. The manual clarifies that CPM means copies per million rather than unnormalized counts per million.
Sources
biobakery/humann: readme.md · readme.md: description, Main workflow, Download the databases and normalization documentation
Profile review details
Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied.
Stable record: discovery-model-humannSpecifications
Inputs, training, access and other details
Explanatory profile: source reviewed · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Model type | Metagenomic functional profiling pipelineSourcesbiobakery/humann: readme.md · readme.md: description, Main workflow, Download the databases and normalization documentation |
| Architecture | Reference-based functional profiling pipeline with nucleotide and translated search against configured databases.Sourcesbiobakery/humann: readme.md · readme.md: description, Main workflow, Download the databases and normalization documentation |
| Inputs | Short DNA/RNA reads or supported preprocessed alignment/profile inputs.Sourcesbiobakery/humann: readme.md · readme.md: description, Main workflow, Download the databases and normalization documentation |
| Outputs | Gene-family and pathway abundance/coverage tables, including organism-stratified outputs.Sourcesbiobakery/humann: readme.md · readme.md: description, Main workflow, Download the databases and normalization documentation |
| Parameters | Inapplicable as a neural parameter count. · Not applicableSourcesbiobakery/humann: readme.md · readme.md: description, Main workflow, Download the databases and normalization documentation |
| Known versions | HUMAnN 3.0 paper and implementation; nucleotide/protein database versions must be preserved separately.Sourcesbiobakery/humann: readme.md · readme.md: description, Main workflow, Download the databases and normalization documentation |
| Training data | ChocoPhlAn and translated protein-search databases are analysis resources, not a universal neural training corpus.Sourcesbiobakery/humann: readme.md · readme.md: description, Main workflow, Download the databases and normalization documentation |
| Training cutoff | Inapplicable to neural pretraining; reference-database and input-data dates must be recorded for each run. · Not applicableSourcesbiobakery/humann: readme.md · readme.md: description, Main workflow, Download the databases and normalization documentation |
| Context limits | Read files and search-database size; no fixed model context.Sourcesbiobakery/humann: readme.md · readme.md: description, Main workflow, Download the databases and normalization documentation |
| Weights licence | Inapplicable: no neural checkpoint for the core profiling pipeline. · Not applicableSourcesbiobakery/humann: readme.md · readme.md: description, Main workflow, Download the databases and normalization documentation |
| Access | Official project documentation and implementation: https://github.com/biobakery/humannSourcesbiobakery/humann: readme.md · readme.md: description, Main workflow, Download the databases and normalization documentation |
| Code licence | MITSourcesbiobakery/humann: LICENSE · LICENSE: licence text |
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
20 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims | biobakery/humann: readme.md readme.md: description, Main workflow, Download the databases and normalization documentation Version: e07b3a34d0b94c09a8ac5d28ff95009611178be2 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram steps ["Community reads","Reference searches","Gene-family quantification","Pathway profiles"] Individual claims | biobakery/humann: readme.md readme.md: description, Main workflow, Download the databases and normalization documentation Version: e07b3a34d0b94c09a8ac5d28ff95009611178be2 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram title HUMAnN workflow Individual claims | biobakery/humann: readme.md readme.md: description, Main workflow, Download the databases and normalization documentation Version: e07b3a34d0b94c09a8ac5d28ff95009611178be2 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Model type Metagenomic functional profiling pipeline Individual claims | biobakery/humann: readme.md readme.md: description, Main workflow, Download the databases and normalization documentation Version: e07b3a34d0b94c09a8ac5d28ff95009611178be2 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Architecture Reference-based functional profiling pipeline with nucleotide and translated search against configured databases. Individual claims | biobakery/humann: readme.md readme.md: description, Main workflow, Download the databases and normalization documentation Version: e07b3a34d0b94c09a8ac5d28ff95009611178be2 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Access Official project documentation and implementation: https://github.com/biobakery/humann Individual claims | biobakery/humann: readme.md readme.md: description, Main workflow, Download the databases and normalization documentation Version: e07b3a34d0b94c09a8ac5d28ff95009611178be2 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Code licence MIT Individual claims | biobakery/humann: LICENSE LICENSE: licence text Version: e07b3a34d0b94c09a8ac5d28ff95009611178be2 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Inputs Short DNA/RNA reads or supported preprocessed alignment/profile inputs. Individual claims | biobakery/humann: readme.md readme.md: description, Main workflow, Download the databases and normalization documentation Version: e07b3a34d0b94c09a8ac5d28ff95009611178be2 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Outputs Gene-family and pathway abundance/coverage tables, including organism-stratified outputs. Individual claims | biobakery/humann: readme.md readme.md: description, Main workflow, Download the databases and normalization documentation Version: e07b3a34d0b94c09a8ac5d28ff95009611178be2 | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Parameters Inapplicable as a neural parameter count. Individual claims | biobakery/humann: readme.md readme.md: description, Main workflow, Download the databases and normalization documentation Version: e07b3a34d0b94c09a8ac5d28ff95009611178be2 | inapplicable automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: discovered
3 source records and release history
- biobakery/humann official source · Original source · e07b3a34d0b94c09a8ac5d28ff95009611178be2
- biobakery/humann: readme.md · Original source · e07b3a34d0b94c09a8ac5d28ff95009611178be2
- biobakery/humann: LICENSE · Original source · e07b3a34d0b94c09a8ac5d28ff95009611178be2
Technical metadata and extraction receipts
Stable ID: discovery-model-humann
- areas
- microbiome
- access
- official_source_linked
- benchmark applicability
- candidate; not evidence of a reported evaluation
- candidate benchmark ids
- None recorded
- entity level
- method
- reported name
- HUMAnN
- version
- Not reported
- historical missing metadata
- checkpoint: unextracted; code licence: unextracted; parameters: unextracted; training cutoff: unextracted; training data: unextracted; version: unextracted; weights licence: unextracted
- metadata review scope
- historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
- legacy kinds
- model
- entity classification
- review date: 2026-09-17; rationale: This record identifies a composed analysis workflow with separately identifiable upstream models, representations or tools and a downstream prediction/scoring procedure. Results belong to that complete composition rather than to an upstream model alone.; source ids: evidence-official-10f58e320879def8b102; source locator: readme.md: description, Main workflow, Download the databases and normalization documentation; ambiguities: None recorded